#####################################################################
# Time-stamp: <2006-09-28 22:00:59 patrick>
#####################################################################
package Config_global;
use strict;

use UNIVERSAL::require;
use Error;

=head1 NAME

Config_global - global EP XML UI configuration options.

=head1 SYNOPSIS

=head1 DESCRIPTION

All these settings can be overridden in the local configuration files
(Config_*), by including this file first in them.

A local configuration file should be linked to C<Config.pm> - this is
searched for at runtime.

=cut

$EP::Config::h->{TMP}        = "$EP::Config::h->{HTML_ROOT}/tmp";
$EP::Config::h->{LOG}        = "$EP::Config::h->{HTML_ROOT}/log";
$EP::Config::h->{CONF}       = "$EP::Config::h->{ROOT}/conf";
$EP::Config::h->{BIN}        = "$EP::Config::h->{ROOT}/cgi-lib/bin";
$EP::Config::h->{RLIB}       = "$EP::Config::h->{ROOT}/cgi-lib/R";
$EP::Config::h->{TMPL}       = "$EP::Config::h->{ROOT}/cgi-lib/tmpl";


$EP::Config::h->{GET_DATA_HREF}     = "$EP::Config::h->{CGI_HREF}/ep_get_data.pl";
$EP::Config::h->{SELECT_ITEMS_HREF} = "$EP::Config::h->{CGI_HREF}/ep_select_items.pl";

$EP::Config::h->{BASIC_XSL}      = "basic_ui.xsl";
$EP::Config::h->{EPC_HELP_XSL}   = "epc_help.xsl";
$EP::Config::h->{SESSIONLOG_XSL} = "session_log.xsl";
$EP::Config::h->{SVG_XSLT}       = "EPGridRenderer.xsl";

$EP::Config::h->{COMPONENTS} =
    {  -1 => "$EP::Config::h->{HTML_ROOT}/static/xml/Basic_Container.epc.xml"
    ,   0 => "$EP::Config::h->{HTML_ROOT}/static/xml/User_Management.epc.xml"
    ,   1 => "$EP::Config::h->{HTML_ROOT}/static/xml/Data_Upload.epc.xml"
    ,   2 => "$EP::Config::h->{HTML_ROOT}/static/xml/Data_Selection.epc.xml"
    ,   3 => "$EP::Config::h->{HTML_ROOT}/static/xml/Hierarchical_Clustering.epc.xml"
    ,   4 => "$EP::Config::h->{HTML_ROOT}/static/xml/Clustering_K_groups.epc.xml"
    ,   5 => "$EP::Config::h->{HTML_ROOT}/static/xml/Descriptive_Statistics.epc.xml"
    ,   6 => "$EP::Config::h->{HTML_ROOT}/static/xml/Between_Group_Analysis.epc.xml"
    ,   7 => "$EP::Config::h->{HTML_ROOT}/static/xml/Ordination.epc.xml"
    ,   8 => "$EP::Config::h->{HTML_ROOT}/static/xml/Data_Transformation.epc.xml"
    ,   9 => "$EP::Config::h->{HTML_ROOT}/static/xml/Clustering_Comparison.epc.xml"
    ,  10 => "$EP::Config::h->{HTML_ROOT}/static/xml/Published_Datasets.epc.xml"
    ,  11 => "$EP::Config::h->{HTML_ROOT}/static/xml/Clustering.epc.xml"
    ,  12 => "$EP::Config::h->{HTML_ROOT}/static/xml/Signature_Algorithm.epc.xml"
    ,  13 => "$EP::Config::h->{HTML_ROOT}/static/xml/Similarity_Search.epc.xml"
    ,  14 => "$EP::Config::h->{HTML_ROOT}/static/xml/Sequence_Motif.epc.xml"
    ,  15 => "$EP::Config::h->{HTML_ROOT}/static/xml/Similarity_Search.vis.xml"
    ,  16 => "$EP::Config::h->{HTML_ROOT}/static/xml/Pattern_Matching.epc.xml"
    ,  17 => "$EP::Config::h->{HTML_ROOT}/static/xml/User_Preferences.epc.xml"
    ,  18 => "$EP::Config::h->{HTML_ROOT}/static/xml/Data_Management.epc.xml"
    ,  20 => "$EP::Config::h->{HTML_ROOT}/static/xml/Results_Display.epc.xml"
    ,  21 => "$EP::Config::h->{HTML_ROOT}/static/xml/Hierarchical_Clustering.vis.xml"
    ,  22 => "$EP::Config::h->{HTML_ROOT}/static/xml/Data_Viewer.epc.xml"
    ,  23 => "$EP::Config::h->{HTML_ROOT}/static/xml/Data_Viewer.vis.xml"
    ,  24 => "$EP::Config::h->{HTML_ROOT}/static/xml/Missing_Value_Imputation.epc.xml"
    ,  25 => "$EP::Config::h->{HTML_ROOT}/static/xml/Experiment_Design.epc.xml"
    ,  26 => "$EP::Config::h->{HTML_ROOT}/static/xml/GO_Annotation.epc.xml"
    ,  27 => "$EP::Config::h->{HTML_ROOT}/static/xml/Sequence_Homology.epc.xml"
    ,  100 => "$EP::Config::h->{HTML_ROOT}/static/xml/Expression_Data_Upload.epc.xml"
    ,  101 => "$EP::Config::h->{HTML_ROOT}/static/xml/Sequence_Data_Upload.epc.xml"
    ,  102 => "$EP::Config::h->{HTML_ROOT}/static/xml/Threeway_Similarity_Analysis.epc.xml"
    ,  103 => "$EP::Config::h->{HTML_ROOT}/static/xml/Sequence_Management.epc.xml"
    ,  104 => "$EP::Config::h->{HTML_ROOT}/static/xml/t-test.epc.xml"
    ,  105 => "$EP::Config::h->{HTML_ROOT}/static/xml/Advanced_Clustering_Comparison.epc.xml"
    ,  106 => "$EP::Config::h->{HTML_ROOT}/static/xml/Chromosome_Localization.epc.xml"
    ,  112 => "$EP::Config::h->{HTML_ROOT}/static/xml/Data_Normalization.epc.xml"
    ,  113 => "$EP::Config::h->{HTML_ROOT}/static/xml/Sequence_Logo.epc.xml"
    ,  150 => "$EP::Config::h->{HTML_ROOT}/static/xml/Dataset_Properties.epc.xml"
    };

$EP::Config::h->{EPC_HELP} = "$EP::Config::h->{HTML_HREF}/static/help";

$EP::Config::h->{WWW_TMP}    = "tmp";

# Directories
$EP::Config::h->{EPNG_PUBDATA_PATH} = "$EP::Config::h->{EPNG_DATA_PATH}/published";
$EP::Config::h->{EPNG_USRDATA_PATH} = "$EP::Config::h->{EPNG_DATA_PATH}/users";
$EP::Config::h->{EPNG_GODATA_PATH} = "$EP::Config::h->{EPNG_DATA_PATH}/GO";

$EP::Config::h->{EPNG_PUBDATA_URL} = "$EP::Config::h->{EPNG_DATA_URL}/published";
$EP::Config::h->{EPNG_USRDATA_URL} = "$EP::Config::h->{EPNG_DATA_URL}/users";

# BioMart configuration
$EP::Config::h->{BioMart} =
    { confFile => "$EP::Config::h->{CONF}/BioMart/defaultMartRegistry.xml"
    , initBatchSize => 100
    , maxBatchSize => 100000
    , virtualSchema => "default"
    , seqType => "transcript_flank"
    , headerAttNames =>
        { coding => [ 'transcript_stable_id', 'gene_stable_id' ]
        , peptide => [ 'transcript_stable_id', 'gene_stable_id', 'translation_stable_id' ]
        , cdna => [ 'transcript_stable_id', 'gene_stable_id' ]
        , transcript_exon => [ 'exon_stable_id', 'gene_stable_id', 'transcript_stable_id' ]
        , gene_exon => [ 'exon_stable_id', 'gene_stable_id' ]
        , gene_exon_intron => ['gene_stable_id']
        , transcript_exon_intron => [ 'transcript_stable_id', 'gene_stable_id' ]
        , transcript_flank => [ 'transcript_stable_id', 'gene_stable_id' ]
        , gene_flank => ['gene_stable_id']
#       , 5utr => [ 'transcript_stable_id', 'gene_stable_id' ]
#       , 3utr => [ 'transcript_stable_id', 'gene_stable_id' ]
        , snp => ['refsnp_id']
        }
    };

# Species related stuff ... probably should go in the database somewhere...
$EP::Config::h->{BASE_ANNOT_IDENTS} = [ "systematicName", "geneSymbol", "interpro", "affymetrix" ];
$EP::Config::h->{SPECIES_METADATA} =
    { agambiae =>
        { scientificName => "Anopheles gambiae"
        , BioMart =>
            { seqDataset => "agambiae_genomic_sequence"
            , structDataset => "agambiae_gene_ensembl_structure"
            , ensDataset => "agambiae_gene_ensembl"
            , xrefType => "gene_stable_id"
            }
        , annot_idents => [ @{$EP::Config::h->{BASE_ANNOT_IDENTS}}, qw ( anoest tigr_aggi ) ]
        }

    , amellifera =>
        { scientificName => "Apis mellifera"
        , BioMart =>
            { seqDataset => "amellifera_genomic_sequence"
            , structDataset => "amellifera_gene_ensembl_structure"
            , ensDataset => "amellifera_gene_ensembl"
            , xrefType => "gene_stable_id"
            }
        }

    , athaliana =>
        { scientificName => "Arabidopsis thaliana"
        , annotationFile => "gene_association.tair"
        , geneUrl => "http://www.arabidopsis.org/servlets/Search?type=general&name=<REPLACE_THIS>&action=detail&method=4&sub_type=gene"
        , nodeUrl => "http://www.ebi.ac.uk/ego/GSearch?query=<REPLACE_THIS>&mode=id"
        , annot_idents => [ @{$EP::Config::h->{BASE_ANNOT_IDENTS}}, qw ( abrc_stock asrp catma nasc tair tair_anat tair_dev tigr_atdb ) ]
        }

    , banthracis =>
        { scientificName => "Bacillus anthracis"
        , annotationFile => "gene_association.tigr_Banthracis"
        , geneUrl => "http://www.tigr.org/tigr-scripts/CMR2/GenePage.spl?locus=<REPLACE_THIS>"
        , nodeUrl => "http://www.ebi.ac.uk/ego/GSearch?query=<REPLACE_THIS>&mode=id"
        }

    , bsubtilis =>
        { scientificName => "Bacillus subtilis" }
    , btaurus =>
        { scientificName => "Bos taurus" }

    , celegans =>
        { scientificName => "Caenorhabditis elegans"
        , annotationFile => "gene_association.wb"
        , geneUrl => "http://www.wormbase.org/db/gene/gene?name=<REPLACE_THIS>"
        , nodeUrl => "http://www.wormbase.org/db/ontology/goterm?name=<REPLACE_THIS>;class=GO_term"
        , BioMart =>
            { seqDataset => "celegans_genomic_sequence"
            , structDataset => "celegans_gene_ensembl_structure"
            , ensDataset => "celegans_gene_ensembl"
            , xrefType => "gene_stable_id"
            }
        , annot_idents => [ @{$EP::Config::h->{BASE_ANNOT_IDENTS}}, qw ( wormbase ) ]
        }

     , cjejuni =>
        { scientificName => "Campylobacter jejuni"
        , annotationFile => "gene_association.tigr_Cjejuni"
        , geneUrl => "http://www.tigr.org/tigr-scripts/CMR2/GenePage.spl?locus=<REPLACE_THIS>"
        , nodeUrl => "http://www.ebi.ac.uk/ego/GSearch?query=<REPLACE_THIS>&mode=id"
        }

    , calbicans =>
        { scientificName => "Candida albicans"
        , annotationFile => "gene_association.cgd"
        , geneUrl => "http://www.candidagenome.org/cgi-bin/locus.pl?locus=<REPLACE_THIS>"
        , nodeUrl => "http://www.candidagenome.org/cgi-bin/GO/go.pl?goid=<REPLACE_THIS>"
        , annot_idents => [ @{$EP::Config::h->{BASE_ANNOT_IDENTS}}, qw (candidadb) ]
        }

    , cfamiliaris =>
        { scientificName => "Canis familiaris"
        , BioMart =>
            { seqDataset => "cfamiliaris_genomic_sequence"
            , structDataset => "cfamiliaris_gene_ensembl_structure"
            , ensDataset => "cfamiliaris_gene_ensembl"
            ,xrefType => "gene_stable_id"
            }
        , annot_idents => [ @{$EP::Config::h->{BASE_ANNOT_IDENTS}}, qw ( vega_cf ) ]
        }

    , cintestinalis =>
        { scientificName => "Ciona intestinalis"
        , BioMart =>
            { seqDataset => "cintestinalis_genomic_sequence"
            , structDataset => "cintestinalis_gene_ensembl_structure"
            , ensDataset => "cintestinalis_gene_ensembl"
            , xrefType => "gene_stable_id"
            }
        }

    , cburnetii =>
        { scientificName => "Coxiella burnetii"
        , annotationFile => "gene_association.tigr_Cburnetii"
        , geneUrl => "http://www.tigr.org/tigr-scripts/CMR2/GenePage.spl?locus=<REPLACE_THIS>"
        , nodeUrl => "http://www.ebi.ac.uk/ego/GSearch?query=<REPLACE_THIS>&mode=id"
        }

    , drerio =>
        { scientificName => "Danio rerio"
        , annotationFile => "gene_association.goa_zebrafish"
        , annotationFileURL => "ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/ZEBRAFISH/gene_association.goa_zebrafish.gz"
        , geneUrl => "http://www.ebi.uniprot.org/entry/<REPLACE_THIS>"
        , nodeUrl => "http://www.ebi.ac.uk/ego/GSearch?query=<REPLACE_THIS>&mode=id"
        , BioMart =>
            { seqDataset => "drerio_genomic_sequence"
            , structDataset => "drerio_gene_ensembl_structure"
            , ensDataset => "drerio_gene_ensembl"
            , xrefType => "gene_stable_id"
            }
        , annot_idents => [ @{$EP::Config::h->{BASE_ANNOT_IDENTS}}, qw ( vega_dr ) ]
        }

    , dethenogenes =>
        { scientificName => "Dehalococcoides ethenogenes"
        , annotationFile => "gene_association.tigr_Dethenogenes"
        , geneUrl => "http://www.tigr.org/tigr-scripts/CMR2/GenePage.spl?locus=<REPLACE_THIS>"
        , nodeUrl => "http://www.ebi.ac.uk/ego/GSearch?query=<REPLACE_THIS>&mode=id"
        }

    , ddiscoideum =>
        { scientificName => "Dictyostelium discoideum"
        , annotationFile => "gene_association.ddb"
        , geneUrl => "http://dictybase.org/db/cgi-bin/gene_page.pl?dictybaseid=<REPLACE_THIS>"
        , nodeUrl => "http://dictybase.org/db/cgi-bin/dictyBase/GO/go.pl?goid=<REPLACE_THIS>&mode=id"
        }

    , dmelanogaster =>
        { scientificName => "Drosophila melanogaster"
        , annotationFile => "gene_association.fb"
        , geneUrl => "http://flybase.bio.indiana.edu/.bin/fbidq.html?<REPLACE_THIS>"
        , nodeUrl => "http://flybase.bio.indiana.edu/.bin/goreport?<REPLACE_THIS>"
        , BioMart =>
            { seqDataset => "dmelanogaster_genomic_sequence"
            , structDataset => "dmelanogaster_gene_ensembl_structure"
            , ensDataset => "dmelanogaster_gene_ensembl"
            , xrefType => "gene_stable_id"
            }
        , annot_idents => [ @{$EP::Config::h->{BASE_ANNOT_IDENTS}}, qw ( flybase flybase_bt flybase_computed_gene flybase_dv) ]
        }

    , egossypii =>
        { scientificName => "Eremothecium gossypii" }

    , ecoli =>
        { scientificName => "Escherichia coli" }

    , ggallus =>
        { scientificName => "Gallus gallus"
        , BioMart =>
            { seqDataset => "ggallus_genomic_sequence"
            , structDataset => "ggallus_gene_ensembl_structure"
            , ensDataset => "ggallus_gene_ensembl"
            , xrefType => "gene_stable_id"
            }
        }

    , gsulfurreducens =>
        { scientificName => "Geobacter sulfurreducens"
        , annotationFile => "gene_association.tigr_Gsulfurreducens"
        , geneUrl => "http://www.tigr.org/tigr-scripts/CMR2/GenePage.spl?locus=<REPLACE_THIS>"
        , nodeUrl => "http://www.ebi.ac.uk/ego/GSearch?query=<REPLACE_THIS>&mode=id"
        }

    , gmorsitans =>
        { scientificName => "Glossina morsitans"
        , annotationFile => "gene_association.GeneDB_tsetse"
        , geneUrl => "http://www.genedb.org/genedb/Search?submit=Search+for&name=<REPLACE_THIS>&organism=glossina&desc=yes&wildcard=yes"
        , nodeUrl => "http://www.genedb.org/amigo/perl/go.cgi?query=<REPLACE_THIS>&species_db=GeneDB_Gmorsitans"
        }

    , gmax =>
        { scientificName => "Glycine max" }

    , hsapiens =>
        { scientificName => "Homo sapiens"
        , annotationFile => "gene_association.goa_human"
        , geneUrl => 'http://www.ebi.uniprot.org/entry/<REPLACE_THIS>'
        , nodeUrl => "http://www.ebi.ac.uk/ego/GSearch?query=<REPLACE_THIS>&mode=id"
        , BioMart =>
            { seqDataset => "hsapiens_genomic_sequence"
            , structDataset => "hsapiens_gene_ensembl_structure"
            , ensDataset => "hsapiens_gene_ensembl"
            , xrefType => "gene_stable_id"
            }
        , annot_idents => [ @{$EP::Config::h->{BASE_ANNOT_IDENTS}}, qw ( sanger tigr_thc vega_hs gdb genecards genew hgmd hgvbase howdy hugo) ]
        }

    , hvulgare =>
        { scientificName => "Hordeum vulgare" }

    , klactis =>
        { scientificName => "Kluyveromyces lactis" }

    , lmajor =>
        { scientificName => "Leishmania major"
        , annotationFile => "gene_association.GeneDB_Lmajor"
        , geneUrl => "http://www.genedb.org/genedb/Search?submit=Search+for&name=<REPLACE_THIS>&organism=leish&desc=yes&wildcard=yes"
        , nodeUrl => "http://www.genedb.org/amigo/perl/go.cgi?query=<REPLACE_THIS>&species_db=GeneDB_Lmajor"
        }

   , lmonocytogenes =>
        { scientificName => "Listeria monocytogenes"
        , annotationFile => "gene_association.tigr_Lmonocytogenes"
        , geneUrl => "http://www.tigr.org/tigr-scripts/CMR2/GenePage.spl?locus=<REPLACE_THIS>"
        , nodeUrl => "http://www.ebi.ac.uk/ego/GSearch?query=<REPLACE_THIS>&mode=id"
        }

    , mgrisea =>
        { scientificName => "Magnaporthe grisea" }

    , mtruncatula =>
        { scientificName => "Medicago truncatula" }

    , mcapsulatus =>
        { scientificName => "Methylococcus capsulatus"
        , annoationFile => "gene_association.tigr_Mcapsulatus"
        , geneUrl => "http://www.tigr.org/tigr-scripts/CMR2/GenePage.spl?locus=<REPLACE_THIS>"
        , nodeUrl => "http://www.ebi.ac.uk/ego/GSearch?query=<REPLACE_THIS>&mode=id"
        }

    , mmusculus =>
        { scientificName => "Mus musculus"
        , annotationFile => "gene_association.goa_mouse"
        , annotationFileURL => "ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/MOUSE/gene_association.goa_mouse.gz"
        , geneUrl => "http://www.informatics.jax.org/javawi2/servlet/WIFetch?page=searchTool&query=<REPLACE_THIS>&selectedQuery=Genes+and+Markers"
        , nodeUrl => "http://www.informatics.jax.org/searches/GO.cgi?id=<REPLACE_THIS>"
# this probably needs an update
#       , GFF_dsn => "dbi:Pg:dbname=mouse_gff;user=postgres"
        , BioMart =>
            { seqDataset => "mmusculus_genomic_sequence"
            , structDataset => "mmusculus_gene_ensembl_structure"
            , ensDataset => "mmusculus_gene_ensembl"
            , xrefType => "gene_stable_id"
            }
        , annot_idents => [ @{$EP::Config::h->{BASE_ANNOT_IDENTS}}, qw ( emap_ts gxd mgd mtb nia_nih tigr_mgi vega_mm) ]
        }

    , ncrassa =>
        { scientificName => "Neurospora crassa" }

    , omykiss =>
        { scientificName => "Oncorhynchus mykiss" }

    , osativa =>
        { scientificName => "Oryza sativa"
        , annotationFile => "gene_association.gramene_oryza"
        , geneUrl => "http://www.gramene.org/gramene/searches/browser?query=<REPLACE_THIS>&RGN=on&search_type=All#"
        , nodeUrl => "http://www.gramene.org/db/ontology/search_term?id=<REPLACE_THIS>"
        }

    , ptroglodytes =>
        { scientificName => "Pan troglodytes"
        , BioMart =>
            { seqDataset => "ptroglodytes_genomic_sequence"
            , structDataset => "ptroglodytes_gene_ensembl_structure"
            , ensDataset => "ptroglodytes_gene_ensembl"
            , xrefType => "gene_stable_id"
            }
        }

    , pfalciparum =>
        { scientificName => "Plasmodium falciparum"
        , annotationFile => "gene_association.GeneDB_Pfalciparum"
        , geneUrl => "http://www.genedb.org/genedb/Search?submit=Search+for&name=<REPLACE_THIS>&organism=malaria&desc=yes&wildcard=yes"
        , nodeUrl => "http://www.genedb.org/amigo/perl/go.cgi?query=<REPLACE_THIS>&species_db=GeneDB_Pfalciparum"
        }

    , paeruginosa =>
        { scientificName => "Pseudomonas aeruginosa" }

    , psyringae =>
        { scientificName => "Pseudomonas syringae"
        , annotationFile => "gene_association.tigr_Psyringae"
        , geneUrl => "http://www.tigr.org/tigr-scripts/CMR2/GenePage.spl?locus=<REPLACE_THIS>"
        , nodeUrl => "http://www.ebi.ac.uk/ego/GSearch?query=<REPLACE_THIS>&mode=id"
        }

    , rnorvegicus =>
        { scientificName => "Rattus norvegicus"
        , annotationFile => "gene_association.goa_rat"
        , annotationFileURL => "ftp://ftp.ebi.ac.uk/pub/databases/GO/goa/RAT/gene_association.goa_rat.gz"
        , geneUrl => "http://www.ebi.uniprot.org/uniprot-srv/uniProtView.do?proteinId=<REPLACE_THIS>"
        , nodeUrl => "http://rgd.mcw.edu/tools/ontology/ont_search.cgi?match_type=equals&search_string=<REPLACE_THIS>&ontology=go"
        , BioMart =>
            { seqDataset => "rnorvegicus_genomic_sequence"
            , structDataset => "rnorvegicus_gene_ensembl_structure"
            , ensDataset => "rnorvegicus_gene_ensembl"
            , xrefType => "gene_stable_id"
            }
        , annot_idents => [ @{$EP::Config::h->{BASE_ANNOT_IDENTS}}, qw ( rgd rgd_qtl) ]
        , preferred_ident => "geneSymbol"
        }

    , rrattus =>
        { scientificName => "Rattus rattus" }

    , scerevisiae =>
        { scientificName => "Saccharomyces cerevisiae"
        , annotationFile => "gene_association.sgd"
        , geneUrl => "http://db.yeastgenome.org/cgi-bin/SGD/locus.pl?locus=<REPLACE_THIS>"
        , nodeUrl => "http://db.yeastgenome.org/cgi-bin/SGD/GO/go.pl?goid=<REPLACE_THIS>"
        , BioMart =>
            { seqDataset => "scerevisiae_genomic_sequence"
            , structDataset => "scerevisiae_gene_ensembl_structure"
            , ensDataset => "scerevisiae_gene_ensembl"
            , xrefType => "gene_stable_id"
            }
        , annot_idents => [ @{$EP::Config::h->{BASE_ANNOT_IDENTS}}, qw ( sgd ) ]
        , preferred_ident => "systematicName"
        }

    , sofficinarum =>
        { scientificName => "Saccharum officinarum" }

    , spombe =>
        { scientificName => "Schizosaccharomyces pombe"
        , annotationFile => "gene_association.GeneDB_Spombe"
        , geneUrl => "http://www.genedb.org/genedb/Search?submit=Search+for&name=<REPLACE_THIS>&organism=pombe&desc=yes&wildcard=yes"
        , nodeUrl => "http://www.genedb.org/amigo/perl/go.cgi?query=<REPLACE_THIS>&species_db=GeneDB_Spombe"
        , annot_idents => [ @{$EP::Config::h->{BASE_ANNOT_IDENTS}}, qw ( genedb) ]
        , preferred_ident => "interpro"
        }

    , soneidensis =>
        { scientificName => "Shewanella oneidensis"
        , annotationFile => "gene_association.tigr_Soneidensis"
        , geneUrl => "http://www.tigr.org/tigr-scripts/CMR2/GenePage.spl?locus=<REPLACE_THIS>"
        , nodeUrl => "http://www.ebi.ac.uk/ego/GSearch?query=<REPLACE_THIS>&mode=id"
        }

    , spomeroyi =>
        { scientificName => "Silicibacter pomeroyi"
        , annotationFile => "gene_association.tigr_Spomeroyi"
        , geneUrl => "http://www.tigr.org/tigr-scripts/CMR2/GenePage.spl?locus=<REPLACE_THIS>"
        , nodeUrl => "http://www.ebi.ac.uk/ego/GSearch?query=<REPLACE_THIS>&mode=id"
        }

    , saureus =>
        { scientificName => "Staphylococcus aureus" }

    , sscrofa =>
        { scientificName => "Sus scrofa" }

    , tnigroviridis =>
        { scientificName => "Tetraodon nigroviridis",
        ,  BioMart =>
            { seqDataset => "tnigroviridis_genomic_sequence"
            , structDataset => "tnigroviridis_gene_ensembl_structure"
            , ensDataset => "tnigroviridis_gene_ensembl"
            , xrefType => "gene_stable_id"
            }
        }

    , trubripes =>
        { scientificName => "Torafugu rubripes"
        , BioMart =>
            { seqDataset => "frubripes_genomic_sequence"
            , structDataset => "frubripes_gene_ensembl_structure"
            , ensDataset => "frubripes_gene_ensembl"
            , xrefType => "gene_stable_id"
            }
        }

    , taestivum =>
        { scientificName => "Triticum aestivum" }

    , tbrucei =>
        { scientificName => "Trypanosoma brucei"
        , annotationFile => "gene_association.GeneDB_Tbrucei"
        , geneUrl => "http://www.genedb.org/genedb/Search?submit=Search+for&name=<REPLACE_THIS>&organism=tryp&desc=yes&wildcard=yes"
        , nodeUrl => "http://www.genedb.org/amigo/perl/go.cgi?query=<REPLACE_THIS>&species_db=GeneDB_Tbrucei"
        }

    , vcholerae =>
        { scientificName => "Vibrio cholerae"
        , annotationFile => "gene_association.tigr_Vcholerae"
        , geneUrl => "http://www.tigr.org/tigr-scripts/CMR2/GenePage.spl?locus=<REPLACE_THIS>"
        , nodeUrl => "http://www.ebi.ac.uk/ego/GSearch?query=<REPLACE_THIS>&mode=id"
        }

    , vvinifera =>
        { scientificName => "Vitis vinifera" }

    , xlaevis =>
        { scientificName => "Xenopus laevis" }

    , xtropicalis =>
        { scientificName => "Xenopus tropicalis"
        , BioMart =>
            { seqDataset => "xtropicalis_genomic_sequence"
            , structDataset => "xtropicalis_gene_ensembl_structure"
            , ensDataset => "xtropicalis_gene_ensembl"
            , xrefType => "gene_stable_id"
            }
        }

    , zmays =>
        { scientificName => "Zea mays" }
    };

# expression data related stuff
$EP::Config::h->{EXP_NRBINS} = 100;

#Password encryption
$EP::Config::h->{SALT} = 10;

#session related stuff
$EP::Config::h->{EXPIRE_SESSION} = 2; # in hours

#Binary programs inside bin
$EP::Config::h->{DISTANCES_CMD}                     = "$EP::Config::h->{BIN}/bin.distances.allall";
$EP::Config::h->{HIERARCHICAL_CLUSTERING_CMD}       = "$EP::Config::h->{BIN}/bin.clustering.hierarchical";
$EP::Config::h->{FAST_HIERARCHICAL_CLUSTERING_CMD}  = "$EP::Config::h->{BIN}/bin.clustering.fasthierarchical";
$EP::Config::h->{KMEANS_CLUSTERING_CMD}             = "$EP::Config::h->{BIN}/bin.clustering.kmeans";
$EP::Config::h->{KMEDOIDS_CLUSTERING_CMD}           = "$EP::Config::h->{BIN}/bin.clustering.kmedoids";
$EP::Config::h->{SPEXS_CMD}                         = "$EP::Config::h->{BIN}/bin.spexs";

$EP::Config::h->{CHROMOSOME_LOCALIZATION_IDEOGRAMS} = "$EP::Config::h->{CONF}/Chromosome_Localization";

$ENV{PGPLOT_BACKGROUND} = 'white';
$ENV{PGPLOT_FOREGROUND} = 'black';

$ENV{R_LIBS} = $EP::Config::h->{RLIB};

$ENV{CLASSPATH} = join ( ":", glob ( "$EP::Config::h->{ROOT}/cgi-lib/java/*.jar" ) );
$ENV{PERL_INLINE_DIRECTORY} = $EP::Config::h->{TMP};

1;
